Fastq and metadata

Good morning to all!
I’m new in QIIME2 analysis, and I wanted to ask how can I associate the .txt mapping file to fastq sequences.

From 45 samples, I obtained 45 fastq.file with Ion Torrent sequencing run. In each fastq.file obtained, barcodes were removed and I don’t get the Barcode.fastq file; I’m trying to remove the primers, and than associate the .txt mapping file (with all information about each sample) to each fastq.

In QIIME I used the split_libraries.py script, but in QIIME2 I have not understood which is the best procedure…

Can someone help me, please?
Any help will be very appreciate

Sara

Hello Sara,

Check out this section on importing fastq files. Does that look like a good fit for your data?

Colin

Thanks @colinbrislawn!

@SDA89, thanks for writing!

Before you get into working with metadata, you will want to import your data — the link @colinbrislawn pointed to is a great start, but before you work on that tutorial, please take a look at the Getting Started guide — it will lead you through the important concepts in QIIME 2 using toy datasets.

It sounds like you have already demultiplexed data, so you will probably want to use one of the fastq manifest formats when importing your data. This format lets you assign sample ids to your individual files.

QIIME 2 doesn’t officially support ion torrent products (mostly just because we haven’t worked with it much), but theoretically you can use q2-dada2 for quality control. Let us know how that goes for you!

After you have worked through the Getting Started guide, and imported your data, then you can learn about Metadata!


I strongly encourage you to get started with the Getting Started guide, and work through all of the tutorials we have made available, before working with your own data. Let us know if you get stuck, and feel free to open a new issue for any new questions! :t_rex:

Dear @thermokarst thank you for your kind and complete reply!

I was using QIIME to analyse my sequence data, obtained from IonTorrent run. Those data are single reads and demultiplexed yet. I completed the Tutorial for understanding how to work with QIIME2 but when I saw that the procedure was a worflow for Illumina data, I was in doubt about how to process my sequences from Ion Torrent!!

Thank you again!!

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Dear @colinbrislawn I will check the section you suggest me! Let’s see if it is good for my data!

Thank you for your reply!!!

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